Saturday, September 26, 2015

Evolution’s Junk Science at the University of Maine

It’s Not About Science

Thinking about taking CHY 431—Structure and Mechanism in Biological Chemistry next semester at the University of Maine? If so you likely will be fed junk evolutionary science like this page:

The page compares the amino acid sequences from the protein cytochrome c across 38 different species. A few of the residues are conserved across all 38 species. For example, position 10 consistently has the amino acid phenylalanine. And what’s the conclusion? That “Clearly, evolution selects against any change at these positions.”

Clearly?

Actually this evolutionary reasoning has long since been demonstrated to be false with another, even more highly conserved protein—histone IV. If this was about science then students would at least learn what the observations, rather than the dogma, have to say.

Furthermore, the idea that the cytochrome c proteins from all of these species (from cows and ducks to yeast, fungus and bacteria) are related via common descent means that evolution must have created cytochrome c very early in evolutionary history. Certainly earlier than the advent of the electron transport chain (ETC) for which cytochrome c plays an important role. In other words, random mutations somehow created cytochrome c (a feat which itself has no scientific explanation), and then eons later the protein just happened to fit in with one of the most fantastic inventions in all of biology.

The serendipity is astonishing.

Later the page discusses the cytochrome c sequence positions that are highly variable. Here the student is told that “evolutionary drift randomizes these residues.” This is unfortunately yet more evolutionary dogma. In fact there is no scientific evidence that these residues have been “randomized.” That notion comes from the belief that evolution is true, in spite of the science. It may be true that those positions are neutral with respect to function and so can be “randomized,” but that is hardly obvious. Evolution has a long history of claiming structures are random and useless junk, only later to be corrected by scientific findings of function.

Finally the page compares the evolutionary tree based on the cytochrome c protein sequences with the traditional evolutionary tree and makes the ridiculously false claim that “Such trees tend to agree closely with those constructed by evolutionary biologists using morphological data, and provide independent evidence of common descent.”

In fact such trees often do not agree closely with trees based on morphological data. The differences are so significant that they cannot be explained merely as evolutionary “noise.” Therefore by modus tollens, according to the page’s own logic, the science falsifies common descent. No sense in telling the students about that though.

51 comments:

Maybe you guys could make sense of this tree using ID ?Why would this protein be different for all those organisms if it has been deisgned ? Then what would those differences tell us about the design ?

You need to provide an alternative explanation if you want your critism to be constructive.

CalamityYour comment reminds me of what an evolutionist said when text books were being criticized for using evidence that was exposed as fraud over 90 years ago for evolution, such as Haeckel's embryos (which are still found in textbooks today). He said, "Well what should we replace it with?"Bogus claims are fine as long as students can be indoctrinated in the "truth".

PhillyMike, I think that you are exaggerating the Haeckel issue. To claim that he intended to be fraudulent has never been proven. What is clear is that his drawings were biased by his expectations. The same sort of thing can be seen in drawings of natives from non-european continents from the 1400s until fairly modern times.

But bias and fraud are two different things. For example, statisticians have estimated that the probability of Mendel obtaining the numbers and ratios that he did would be extremely low. But nobody is suggesting that this was the result of intentional fraud.

My biology education took place during the mid 70s to the mid 80s. I remember seeing these drawings, but I also remember being told that Haeckel's theory was no longer accepted.

Personally, I would like to see the drawings retained in text books as an object lesson in the hazards of bias.

No, these variable residues have been shown empirically (in yeast) to not affect function. The ETC is a heavily studied mechanism, and if you want to claim that the requirements of CytC are materially different across different species then you are going to need to propose something specific because the evidence is firmly in the other direction.

You will also need to explain the perfect correlation of function CytC sequences in this yeast experiment with function sequences found in other animals, and the fact that none of the non-functional sequences in yeast can be found in the wild.

"Common designer" is clutching at straws. As Calamity says, you need to explain why this tree can be created at all; why the designer chose different sequences to perform the same task.

What??? You first said "the protein is different in different organisms due to the organisms needs". And then you said "I didn't say anything about affecting function". On what grounds are you inferring a common designer when these differences do not contribute to function or purpose? It's a contradiction in terms in my book.

"How can the differences in a protein that functions the same produce the morphological differences observed?"

THEY DON'T, AND THAT IS THE POINT!

These differences DON'T affect function and they DON'T affect morphology, so you need to explain why they can be constructed as a tree that DOES reflect the morphological differences.

hi glenn. the answer is that this sequence indeed have a small effect in the specific species. by the way- cytochrome b give us a different tree from the cytochrome c phylogeny ( Michael S. Y. Lee, "Molecular phylogenies become functional," Trends in Ecology and Evolution, Vol)

Given that we are talking about the protein sequences, I can't even make sense of that statement. Please try again.

"Also it's a common DESIGN, not a common designER."

Fine, I'll even grant you for the sake of argument that the invariant residues could come be a common design. You now have the problem of explaining why the variant residues fall into such a pattern that reflects morphology, when those variant residues have been shown empirically to not affect functions.

"And again the differences are due to the different requirements of the other proteins that sequence is used in."

What are you talking about?

"That's retarded. If the differences don't make a difference then the tree should reflect that."

If creation was true, yes there would be no reason why the chimp sequence would be identical to the human sequence. If creation were true, I would expect an entirely random tree (or perhaps no tree at all if the designer decided to put the same sequence in all species).

On the other hand, if common descent were true I would expect that (due to drift and fixation) the variant residues would reflect the relationship between species.

It is the fact that this CytC tree broadly matches trees built from independent data that you have to explain. It doesn't make sense unless common descent is true.

Glenn:Given that we are talking about the protein sequences, I can't even make sense of that statement.

That's your problem. One of many.

You said something about function. The sequence is different but the function isn't.

Fine, I'll even grant you for the sake of argument that the invariant residues could come be a common design. You now have the problem of explaining why the variant residues fall into such a pattern that reflects morphology, when those variant residues have been shown empirically to not affect functions.

I would say that you have to explain why you think such a tree would be observed given the fact that the function is the same.

With a common design we see the differences- cars and trucks are mostly similar with the differences owing to different requirements.

What are you talking about?

genetics- alternative splicing and overlapping.

If creation was true, yes there would be no reason why the chimp sequence would be identical to the human sequence.

It isn't identical and a COMMON DESIGN says why they would be similar

If creation were true, I would expect an entirely random tree

Obviously you have never worked on a big construction project. The tree comes first and the design implemented to fill it.

On the other hand, if common descent were true I would expect that (due to drift and fixation) the variant residues would reflect the relationship between species.

I would expect molecular clocks to be saturated and as such unable to tell us anything about the relationships.

You said something about function. The sequence is different but the function isn't.

Exactly! Why are there different sequences for the same function? This is the question I'm asking you to answer from a creation/ID standpoint. Common descent answers it easily.

I would say that you have to explain why you think such a tree would be observed given the fact that the function is the same.

Because the variant residues (which don't affect function) reflect the mutations shared by common ancestors. Like I've said in previous posts, this is some of the best evidence you can get for common descent. I have absolutely no problem explaining it, but I can't even conceive of an explanation from a creationist/ID standpoint.

With a common design we see the differences- cars and trucks are mostly similar with the differences owing to different requirements.

Sure, but in this case the function is the same, and there are billions upon billions of sequences that can perform this function. So, why, among so any possible sequences, did your designer choose to lay them out in such a way that its tree would match a morphological tree?

It isn't identical and a COMMON DESIGN says why they would be similar

Please continue that thought by telling is how a COMMON DESIGN why explains the differences.

Obviously you have never worked on a big construction project. The tree comes first and the design implemented to fill it.

That makes absolutely no sense. What is the purpose of the tree in the first place when literally any configuration would work? Why would a designer choose a tree?

I would expect molecular clocks to be saturated and as such unable to tell us anything about the relationships.

You can see saturation start to kick in at around the kingdom level (for example, comparing yeast to animals) but the animal sequences are clearly not saturated, so I guess your expectations are wrong.

I do, but I fail to see how this is relevant when we are comparing a single transcript across multiple species.

"Common descent answers it easily."

No, it doesn't.

From the guy that says "they're different because they can be". Common descent draws on empirical observations (mutation, drift, fixation) while your response doesn't even qualify as an explanation. It explains nothing. Why is the chimpanzee sequence closer to the human sequence than it is to the whale sequence, when all three are functionally equivalent? Try again.

Or not. Because it's pretty clear that you don't WANT to understand it.

"The three aren't functionally equivalent. Even a child can see that a chimp looks more like a human than a whale."

Yes they are functionally equivalent. Please read the study I posted.

Of course a chimp looks more like a human than a whale. I don't even think you realise it, but you're making an implicit causal relationship between the requirements of an organism (or it's morphology) and its CytC sequence, when it is demonstrable that no such relationship exists.

I can only phrase it in so many ways before I have to conclude that you're just not bright enough to understand it.

Try answering the question again, but this time think before you type. Why is the chimpanzee sequence closer to the human sequence than it is to the whale sequence, when all three are functionally equivalent?

Glen: "I can only phrase it in so many ways before I have to conclude that you're just not bright enough to understand it."

I was wondering when you would come to this conclusion. It is nice to see that it took you no longer than it has taken any other intelligent human being to conclude that Joe deserves sympathy, but not intellectual respect.

Glenn:We are comparing the same transcripts. The differences in these transcripts between species are not due to alternative splicing. They are due to variations in the underlying DNA, and demonstrably so.

You are a moron. The differences are to facilitate alternative splicing. The differences allow for different proteins from those differing transcripts.

PhillyMike, thank you for the link. I was aware that his drawings were exaggerated, but I was not aware that he admitted to doing it intentionally.

As I mentioned, I was taught that they were not accurate and that his theory was discarded shortly after he proposed it. Honestly, I don't recall what the text in the text books said. But, obviously, Miller and Levine corrected it in their book.

Unfortunately, text books (in all fields) are notorious for being seriously out of date. I remember taking an oceanography course in 1979 or 1980 and the text book was published in 1936. The people who write text books draw heavily from historic work, as they should, and don't always give it the scrutiny that they should. But it is a far cry to equate inadequate oversight by the author and editors to intentionally trying to mislead.

Mislead? To declare the theories of evolution to impressionable children as the truth in the textbooks, making them memorize evolutionary doctrines as fact to be able to pass their exams is not misleading it's reprehensible. I have friends who in college were told in no uncertain terms that if they expressed dissent over the theory they wouldn't pass the course. Seems there's a problem that permeates the field.

If you take a course on chemistry and you spout alchemy, you will fail. If you take a course in theology and spout atheism, you will fail. When you take a course in history of the second world war and spout holocaust denial, you will fail. When you take a course in physics and argue that angels push the planets and stars around, you will fail. If you take a course in ID and spout evolution you will fail. Why should a course on evolution be any different? You take courses in any subject you do it to learn about the theory and evidence supporting it.

I took several evolution courses and there was plenty of opportunity do discuss the theory and any alternatives. But when a question is asked about genetic drift, or natural selection, you can't respond that it doesn't exist and that it is all designed. Any more than you could answer a question about gravity in a physics exam by saying that gravity doesn't exist, the world sucks.

These variable residues ARE "junk", at least in the sense that they are selectively neutral (but not in the sense that you can just remove them). Cornelius, this article is an excellent method to demonstrate common descent.

how do you know that those amino acid are neutral? you can even change the whole amino acid chain in a protein and it will still kip the same function. but it will have a small effect. you can replace a lot of parts in a car and it will still function as a car. but it will be a little different.

Pages 3264 is the page you should look at: it shows which variants they tested, against which variants are found in the wild. You'll see that any variants that impacted function were NOT found in the wild.

Combine this with the table on page 3266 and you've got incredibly strong evidence that the selective pressures on CytC are the same in ALL species.

I think trying to debuke textbooks example is not the way to go Mr Hunter. If they are in textbooks it's because they are clear example that are suited for students.

Anybody with an open mind would realise that the case for evolution and common descent of this example is convincing. Of course you could also turn a blind eye and play it mala fide.

Then again ID can't really make sense of this cytc example. With ID you can't predict that the phylogeny of cytC should correspond to the apparent tree of life. Or design take the disguide of common descent. Again since there is no explicit theory of ID we can't say anything constructive nor have some predictive power.

glenn. even if you change an amino acid and get the same protein its not mean that they identical, we know that even a codon that code for the same amino acid can effect the regulation of the protein. so you dont have any evidence that this protein work the same.

now, if evolution isnt true, what evidence we will need to find from a phylogenetic prespective?